dist.matrix.prep.v3: dist.matrix.prep.v3

Description Usage Arguments Value Examples

View source: R/TreCCAtree.R

Description

This is an important internal function to calculate distance matrix, it is used particularly in Tree.build.2nd.treemaking

Usage

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dist.matrix.prep.v3(binary.primary, datainfo.col1 = c("res.0.6", "nUMI",
  "Sample"), datainfo.col2 = c("res.0.6", "nUMI", "Sample"),
  datainfo.col.dog = c("res.0.6", "nUMI", "Sample"),
  cluster.col1 = "res.0.6", cluster.col2 = "res.0.6",
  cluster.col.dog = "res.0.6", withsingledog = F,
  dog.seurat.ob = NULL, neighborwithdog.seurat.ob = NULL)

Arguments

binary.primary

This is the primary clustering result that can be retrieved from Tree.build.prepare object. (Because Tree.build.prepare mainly do the primary clustering.)The input here is tree.prep.ob$primary.total

datainfo.col1

default is c("res.0.6","nUMI","Sample")

datainfo.col2

default is c("res.0.6","nUMI","Sample")

datainfo.col.dog

c("res.0.6","nUMI","Sample")

cluster.col1

default is "res.0.6"

cluster.col2

default is "res.0.6"

cluster.col.dog

"res.0.6"

withsingledog

Default is F

dog.seurat.ob

=NULL

neighborwithdog.seurat.ob

=NULL

Value

This will return an object used for Tree.build.2nd.treemaking

Examples

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 	total.dist.matrxes<-dist.matrix.prep(primary.total,datainfo.col1=c(paste("res.",first.reso[1],sep=""),"nUMI","Sample"),cluster.col1=paste("res.",first.reso[1],sep=""),datainfo.col2=c(paste("res.",first.reso[2],sep=""),"nUMI","Sample"),cluster.col2=paste("res.",first.reso[2],sep=""),res1=paste("res.",first.reso[1],sep=""),res2=paste("res.",first.reso[2],sep=""))

chenweng1991/EZsinglecell documentation built on July 11, 2020, 3:23 p.m.